ID   TRUD_HYDCU              Reviewed;         346 AA.
AC   Q31J61;
DT   04-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT   06-DEC-2005, sequence version 1.
DT   25-MAY-2022, entry version 86.
DE   RecName: Full=tRNA pseudouridine synthase D {ECO:0000255|HAMAP-Rule:MF_01082};
DE            EC=5.4.99.27 {ECO:0000255|HAMAP-Rule:MF_01082};
DE   AltName: Full=tRNA pseudouridine(13) synthase {ECO:0000255|HAMAP-Rule:MF_01082};
DE   AltName: Full=tRNA pseudouridylate synthase D {ECO:0000255|HAMAP-Rule:MF_01082};
DE   AltName: Full=tRNA-uridine isomerase D {ECO:0000255|HAMAP-Rule:MF_01082};
GN   Name=truD {ECO:0000255|HAMAP-Rule:MF_01082}; OrderedLocusNames=Tcr_0216;
OS   Hydrogenovibrio crunogenus (strain DSM 25203 / XCL-2) (Thiomicrospira
OS   crunogena).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Thiotrichales;
OC   Piscirickettsiaceae; Hydrogenovibrio.
OX   NCBI_TaxID=317025;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 25203 / XCL-2;
RX   PubMed=17105352; DOI=10.1371/journal.pbio.0040383;
RA   Scott K.M., Sievert S.M., Abril F.N., Ball L.A., Barrett C.J., Blake R.A.,
RA   Boller A.J., Chain P.S.G., Clark J.A., Davis C.R., Detter C., Do K.F.,
RA   Dobrinski K.P., Faza B.I., Fitzpatrick K.A., Freyermuth S.K., Harmer T.L.,
RA   Hauser L.J., Huegler M., Kerfeld C.A., Klotz M.G., Kong W.W., Land M.,
RA   Lapidus A., Larimer F.W., Longo D.L., Lucas S., Malfatti S.A., Massey S.E.,
RA   Martin D.D., McCuddin Z., Meyer F., Moore J.L., Ocampo L.H. Jr., Paul J.H.,
RA   Paulsen I.T., Reep D.K., Ren Q., Ross R.L., Sato P.Y., Thomas P.,
RA   Tinkham L.E., Zeruth G.T.;
RT   "The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena
RT   XCL-2.";
RL   PLoS Biol. 4:1-17(2006).
CC   -!- FUNCTION: Responsible for synthesis of pseudouridine from uracil-13 in
CC       transfer RNAs. {ECO:0000255|HAMAP-Rule:MF_01082}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=uridine(13) in tRNA = pseudouridine(13) in tRNA;
CC         Xref=Rhea:RHEA:42540, Rhea:RHEA-COMP:10105, Rhea:RHEA-COMP:10106,
CC         ChEBI:CHEBI:65314, ChEBI:CHEBI:65315; EC=5.4.99.27;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01082};
CC   -!- SIMILARITY: Belongs to the pseudouridine synthase TruD family.
CC       {ECO:0000255|HAMAP-Rule:MF_01082}.
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DR   EMBL; CP000109; ABB40812.1; -; Genomic_DNA.
DR   RefSeq; WP_011369638.1; NC_007520.2.
DR   AlphaFoldDB; Q31J61; -.
DR   SMR; Q31J61; -.
DR   STRING; 317025.Tcr_0216; -.
DR   EnsemblBacteria; ABB40812; ABB40812; Tcr_0216.
DR   KEGG; tcx:Tcr_0216; -.
DR   eggNOG; COG0585; Bacteria.
DR   HOGENOM; CLU_005281_4_0_6; -.
DR   OMA; LWLWVEK; -.
DR   OrthoDB; 1490777at2; -.
DR   GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR   GO; GO:0106029; F:tRNA pseudouridine synthase activity; IEA:UniProtKB-EC.
DR   GO; GO:0031119; P:tRNA pseudouridine synthesis; IEA:UniProtKB-UniRule.
DR   Gene3D; 3.30.2340.10; -; 1.
DR   Gene3D; 3.30.2350.20; -; 1.
DR   HAMAP; MF_01082; TruD; 1.
DR   InterPro; IPR020103; PsdUridine_synth_cat_dom_sf.
DR   InterPro; IPR001656; PsdUridine_synth_TruD.
DR   InterPro; IPR011760; PsdUridine_synth_TruD_insert.
DR   InterPro; IPR042214; TruD_catalytic.
DR   InterPro; IPR043165; TruD_insert_sf.
DR   Pfam; PF01142; TruD; 2.
DR   SUPFAM; SSF55120; SSF55120; 1.
DR   TIGRFAMs; TIGR00094; tRNA_TruD_broad; 1.
DR   PROSITE; PS50984; TRUD; 1.
PE   3: Inferred from homology;
KW   Isomerase; tRNA processing.
FT   CHAIN           1..346
FT                   /note="tRNA pseudouridine synthase D"
FT                   /id="PRO_0000230154"
FT   DOMAIN          159..305
FT                   /note="TRUD"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   ACT_SITE        83
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
SQ   SEQUENCE   346 AA;  38935 MW;  2DEC89A2B1BE1D33 CRC64;
     MPNPISLSHF AFAYGRPENT AVLKAEPADF QVDEHIAYTL SGEGEHLWVW VQKIGQNTDW
     VAKQIASWAG ITAKEMGVAG KKDRQAITRQ WMSLHLPGKQ APDIGSLDVP GVTLLKAMRH
     HRKLQTGGLS GNRFTLVLRE INGNLDQIET RLQKIAGKGV PNYFGEQRFG NDFQNLAKAT
     ALFQGQIKSP KRHQKSLYIS AARSWIFNEI LSQRVRQGTW NRAISGDVFQ LEGSQKWFAD
     DSDPSLSKRV EEKGLHPTGA LTGRGVLPSQ SDAFQVEQAV LEKHPFWQAG LEKLGLKQER
     RALRVLPKEM HWEWLDQQTL SVGFDLPAGS YATMVMRELF EVKLED